I'll be honest it does kind of bother me that it is possible to be a -6/-6 as a dirty freeborn or a -7/-7 if a tankborn clanner
It may be simply a case of getting used to running Old School style. Way back in the day, FASA used to have truly elite MW's have skill levels in the negatives. Plus, it's not like those types of MW's are a dime a dozen.
For an "average" MW (which is an above average human), you need the almost unheard of skill level of 9+ to go into the negatives. To drive that lower, you need to have abnormally high attributes which means you're an even smaller portion of the already very unusual and very small population.
Now consider the total number of MW's in the IS. In the 3060's, there were roughly 120 mech regiments in every IS House, plus Mercs, S7 Jocks, and Various Minor Powers (FRR, C*,WOB ect.). Let's be generous and say that works out to 1200 mech regiments. At ~120 mechs per regiment that's a pool of ~150,000 total mechwarriors. Based off various charts in the BT game it looks like a MW with a 0 level skill occurs about 2.67% of the time so that would be a pool of 4,000 MW's. Now that's just for a 0 level to go negative, it'd be an even smaller portion. Let's say a skill 9+ MW is twice as rare as one with a 8+(what you need to have a BT score of 0). That's 1.33% of all IS MW's and a pool of only around 2000.
Now let's figure in the ATT's. Human physical ability scores tend to be based off a bell curve. Ordinarily I'd expect to see a /single/ ATT of 7 in only about 1/3rd the population. So now we're down to 0.445% of the total IS MW population so that's only 668 scattered across the Sphere. Now we are down to a really fuzzy area where you're having to estimate the frequency of multiple high physical characteristics. Best case scenario would probably leave you with a total population of ~222 MW's while more realisitc cases would probably reduced that number down to 1 in 100 or 1000 thousand.
The Cliff Notes Version: Go ahead and allow negative skill levels because at any given time, an IS House probably has at most 1 to 2 of these MW paragons.
-Jackmc